Genome-Based Taxonomy of Species in the Pseudomonas syringae and Pseudomonas lutea Phylogenetic Groups and Proposal of Pseudomonas maioricensis sp. nov., Isolated from Agricultural Soil

Abstract

Species in the phylogenetic group Pseudomonas syringae are considered the most relevant plant pathogenic bacteria, but their taxonomy is still controversial. Twenty named species are validated in the current taxonomy of this group and in recent years many strains have been genome-sequenced, putative new species have been proposed and an update in the taxonomy is needed. A taxonomic study based on the core-genome phylogeny, genomic indices (ANI and GGDC) and gene content (phyletic pattern and Jaccard index) have been applied to clarify the taxonomy of the group. A phylogenomic analysis demonstrates that at least 50 phylogenomic species can be delineated within the group and that many strains whose genomes have been deposited in the databases are not correctly classified at the species level. Other species names, like "Pseudomonas coronafaciens", have been proposed but are not validated yet. One of the putative new species is taxonomically described, and the name Pseudomonas maioricensis sp. nov. is proposed. The taxonomies of Pseudomonas avellanae and Pseudomonas viridiflava are discussed in detail as case studies. Correct strain identification is a prerequisite for many studies, and therefore, criteria are given to facilitate identification.

Keywords: Pseudomonas maioricensis; Pseudomonas syringae; phylogenomics; taxonomy.

Figure 1

RAxML phylogenetic tree (1505 core genes) of representative strains in the P. syringae and P. lutea phylogenetic groups with P. aeruginosa as the outgroup. The numbers in the nodes are bootstrap values of 100 replicates. Main phylogenetic branches are labelled in different colours.

Figure 2

RAxML phylogenetic tree (2015 genes of the core proteome) of representative strains in the P. syringae and P. lutea phylogenetic groups without an outgroup. Main phylogenetic branches are labelled in different colours.

Figure 3

Dendrogram of the ANI values among the strains studied. Type strains are highlighted in bold. Main phylogenetic branches are labelled in different colours. Red line: species threshold. Scale: ANI distance.

Figure 4

Gene content distribution of the 23,319 orthologues calculated by M1CR0B1AL1Z3R, represented by the Jaccard index (a) (discontinuous red line indicates the 6 main phylogenetic branches), a split-tree decomposition (b) and a heatmap (c). Each phylogenetic branch is highlighted with a different colour. Numbers indicate the strain in Table 1.

Figure 5

Venn diagram of the orthologous genes shared by the strains studied in the P. caspiana branch.

Figure 6

Organisation of the P. maioricensis S25T T2SS (a) and T6SS-I (b) clusters and flanking regions. Arrows indicate the detected ORFs and their direction of transcription. The red square indicates a possible gene duplication in P. maioricensis S25T that was absent in P. caspiana FB102T.